Lossless audio on my iPhone

not sure why you had to downgrade to itunes 11, although i hate itunes 12 with a vengeance myself.
itunes does not encode or decode flac, you'll need other program. xld works great:
http://tmkk.undo.jp/xld/index_e.html

if you are deep into apple ecosystem like myself, i suggest you convert everything into apple lossless. since it is lossless, you can convert it back to flac or any lossless formats without losing sound quality, so there is no risk.

I don't think there are many around hear who use lossless audio on I devices. I do but unfortunately I can't help, because I keep all my files in flac, I use an app called golden ear to play them. and to actually get the files into golden ear I either use a program on my pc called iexplorer to copy folders to the golden ear app rather than iTunes, or I start the golden ear ftp server and just upload the files to it over my local network. However if you decide to use these methods I am happy to help, personally I would suggest using golden ear might be better as no idea how to copy tag structure across or guarantee you will have unchanged files. Also remember if your converting files you will then have two sets unless you plan to get rid of your flacs. I would say its probably just easier to use golden ear and either upload folders to it through its ftp server or to use iexplorer to get the content into it.

one thing to bear in mind with syncing stuff through iTunes is the more stuff you have on your device the longer syncing takes the more stuff you have, also the longer backups take as well.
as your phone is backed up whenever you go to sync, with golden ear you can disable iTunes backing up so it will speed your backup and sync ttimes, of course this does rely on you doing your own backups of files but its what I choose to do.
You could use iTunes to import flac files to golden ear but the problem with iTunes is you can't import actual folders, iTunes can dump files on the device, but with my methods you can keep the folder structure intact, it might be worth you having a look at golden ears feature list so you can work out if it meets your playback needs, it offers several ways of browsing your music.
The developer is extremely friendly and helpful and has put a lot of work into making sure his app remains fully accessible with VoiceOver and is good at answering questions and listening to suggestions I was able to work with him very closely on the last big update to ensure the app was totally VoiceOver accessible.
One thing to bear in mind with golden ear is it is a flac player it doesn't have any fancy effects like eq or treble or other artificial things you might want to enhance your music with.
I can't comment at all on the music app because I don't use it at all as I keep all my stuff in flac or mp3.
golden ear does support several different lossless and lossy formats.
One nice thing about golden ear over other flac players is the gapless playback really works I have scene loads of app which claim gapless playback which just doesn't work I can notice even slight gaps.
Regarding file size that depends on the stuff being encoded in the files and the compression level used when creating the files, a good place if your interested in comparing format differences is the hydrogen audio forums
http://www.hydrogenaud.io/forums/
they have loads of stuff about compression formats but to be honest I would say your stuff is already in flac, your happy with it as it is, why create loads of work for yourself buy trying to convert it, thinking its OK then maybe a few months into the process or years down the line after you get rid of your flacs you find out its not how you want.

no sorry the program I use on my pc is called iexplorer and can be grabbed from
www.macroplant.com
to find golden ear have a look in the app directory entry on applevis.
a tip if your looking for an ios app is if your googling for it don't just search for the app name, but search for something like iTunes store followed buy your app name, so iTunes store golden ear.
and it isn't a loud speaker company iexploer and golden ear are made buy totally separate people.

I would say you should keep iTunes around as that's still how you will back your phone up unless of course you use iCloud. but its entirely up to you, if your not sure might be worth emailing macroplant support. They are very helpful, and I have also been working with them closely to improve iexplorer accessibility with jaws. I am sure they would be delighted to hear from another blind user. I still have iTunes on my pc as I refuse to use iCloud.

Hi, you need to right click the golden ear app in the directory tree and choose the option mount as disk, then it will ask if you automatically want to mount this folder whenever the iphone is connected, its up to you if you say yes or no, once you mount the folder it should then automatically open a window entitled golden ear followed by the drive letter, you then use copy and paste after that to get your folders in there. Alternatively I did find out how to sync folders to apps using iTunes but I still prefer windows explorer as its not easy to monitor how the sync is going with iTunes and also it doesn't play a sound once the sync finishes. alternatively golden ear has an ftp server built in which when you start it would allow you to upload files to it through an ftp client, but I have found the ftp unreliable, this doesn't mean you will though if you choose to use it. Uploading through ftp would be slower than usb though as wifi is slower than usb.